|
| Status |
Public on Jul 09, 2012 |
| Title |
E2A RPMI-8402_ChipSeq, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
T-ALL cell line, E2A ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RPMI-8402
cell type: T-cell acute lymphoblastic leukemia (T-ALL) cells
chip antibody: TCF3/E2A
antibody vendor: Santa Cruz
antibody catalog number (lot#): sc-349x (D2109)
|
| Growth protocol |
Human RPMI-8402 cells were purchased from the German Collection of Microorganisms and Cell Culture (DSMZ), Leibniz, Germany. Cells were maintained under typical conditions in RPMI media with 10% bovine calf serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linking with formaldehyde for 20 min.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts (WCEs) were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 4500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing using the Beckman SPRIworks fragment library system with adapters from the Illumina TruSeq DNA kit. DNA fragments were end repaired, ligated and size selected using SPRIworks. DNA was then subjected to 18 cycles of PCR using oligos provided by Illumina.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Chromatin IP against E2A RPMI-8402.
09162011_C0082ABXX_4.ATCACG
Barcode (already removed): ATCACG
|
| Data processing |
Images analysis and base calling were done using the Solexa pipeline.
Reads were aligned to human genome build hg18 using Bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: Aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
|
| |
|
| Submission date |
Jul 08, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE39179 |
TAL1 complex in human T-cell acute lymphoblastic leukemia (RPMI-8402) |
|
| Relations |
| SRA |
SRX158106 |
| BioSample |
SAMN01086121 |
